Dataset Information

MMDB: Entrez's 3D-structure database.

ABSTRACT: Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. To this end, Entrez's search engine provides several powerful features: (i) links between databases, for example between a protein's sequence and structure; (ii) pre-computed sequence and structure neighbors; and (iii) structure and sequence/structure alignment visualization. Here, we focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative analysis. MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html.

SUBMITTER: Chen J

PROVIDER: S-EPMC165533 | biostudies-literature | 2003 Jan

REPOSITORIES: biostudies-literature

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Publications

MMDB: Entrez's 3D-structure database.

Chen Jie J Anderson John B JB DeWeese-Scott Carol C Fedorova Natalie D ND Geer Lewis Y LY He Siqian S Hurwitz David I DI Jackson John D JD Jacobs Aviva R AR Lanczycki Christopher J CJ Liebert Cynthia A CA Liu Chunlei C Madej Thomas T Marchler-Bauer Aron A Marchler Gabriele H GH Mazumder Raja R Nikolskaya Anastasia N AN Rao Bachoti S BS Panchenko Anna R AR Shoemaker Benjamin A BA Simonyan Vahan V Song James S JS Thiessen Paul A PA Vasudevan Sona S Wang Yanli Y Yamashita Roxanne A RA Yin Jodie J JJ Bryant Stephen H SH

Nucleic acids research 20030101 1

Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. To this end, Entrez's search engine provides several powerful features: (i) links between databases, for example between a protein's sequence and structure; ...[more]

PMID: 12520055

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Project description:Post-translational modifications (PTMs) play very important roles in various cell signaling pathways and biological process. Due to PTMs' extremely important roles, many major PTMs have been studied, while the functional and mechanical characterization of major PTMs is well documented in several databases. However, most currently available databases mainly focus on protein sequences, while the real 3D structures of PTMs have been largely ignored. Therefore, studies of PTMs 3D structural signatures have been severely limited by the deficiency of the data. Here, we develop PRISMOID, a novel publicly available and free 3D structure database for a wide range of PTMs. PRISMOID represents an up-to-date and interactive online knowledge base with specific focus on 3D structural contexts of PTMs sites and mutations that occur on PTMs and in the close proximity of PTM sites with functional impact. The first version of PRISMOID encompasses 17 145 non-redundant modification sites on 3919 related protein 3D structure entries pertaining to 37 different types of PTMs. Our entry web page is organized in a comprehensive manner, including detailed PTM annotation on the 3D structure and biological information in terms of mutations affecting PTMs, secondary structure features and per-residue solvent accessibility features of PTM sites, domain context, predicted natively disordered regions and sequence alignments. In addition, high-definition JavaScript packages are employed to enhance information visualization in PRISMOID. PRISMOID equips a variety of interactive and customizable search options and data browsing functions; these capabilities allow users to access data via keyword, ID and advanced options combination search in an efficient and user-friendly way. A download page is also provided to enable users to download the SQL file, computational structural features and PTM sites' data. We anticipate PRISMOID will swiftly become an invaluable online resource, assisting both biologists and bioinformaticians to conduct experiments and develop applications supporting discovery efforts in the sequence-structural-functional relationship of PTMs and providing important insight into mutations and PTM sites interaction mechanisms. The PRISMOID database is freely accessible at http://prismoid.erc.monash.edu/. The database and web interface are implemented in MySQL, JSP, JavaScript and HTML with all major browsers supported.

Dataset Information

MMDB: Entrez's 3D-structure database.

Publications

MMDB: Entrez's 3D-structure database.

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